Name: RenLab-HiC-cortex, Rep1

Organism: Mus musculus

Source: Mouse ES

RE: HindIII

Sample ID: GSM892304

Mapping Statistics

File SRR442145 SRR442146 SRR442147 SRR442148 SRR442149
Total reads 58,553,203 56,102,527 57,935,274 57,089,636 86,465,083
First pair aligned 51,602,560 (88.13%) 49,880,384 (88.91%) 51,893,560 (89.57%) 51,099,917 (89.51%) 76,929,800 (88.97%)
Second pair aligned 47,885,771 (81.78%) 48,755,715 (86.90%) 51,101,055 (88.20%) 50,370,013 (88.23%) 75,110,991 (86.87%)
PCR duplicate paired reads 1,788,981 (3.06%) 1,826,462 (3.26%) 2,007,510 (3.47%) 1,963,802 (3.44%) 3,743,746 (4.33%)
Chimeric paired reads 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
Valid chimeric paired reads 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
Total mapped/paired reads 31,029,410 (52.99%) 31,660,555 (56.43%) 33,138,817 (57.20%) 32,638,099 (57.17%) 48,713,987 (56.34%)
Valid mapped/paired reads 29,240,429 (49.94%) 29,834,093 (53.18%) 31,131,307 (53.73%) 30,674,297 (53.73%) 44,970,241 (52.01%)

File SRR442150
Total reads 85,145,369
First pair aligned 75,767,102 (88.99%)
Second pair aligned 73,952,985 (86.85%)
PCR duplicate paired reads 3,663,545 (4.30%)
Chimeric paired reads 0 (0.00%)
Valid chimeric paired reads 0 (0.00%)
Total mapped/paired reads 47,986,086 (56.36%)
Valid mapped/paired reads 44,322,541 (52.06%)

HiC Read Statistics

Total reads 210,172,908
Chromosome not in fends 0 (0.00%)
PCR duplicates 0 (0.00%)
Outide RE cutsite range 4,309,324 (2.05%)
Insert larger than cutoff 91,118,809 (43.35%)
Fragment circularization 2,377,450 (1.13%)
Possible failed RE digest 22,524,868 (10.72%)
Valid cis reads 29,231,199 (13.91%)
Valid trans reads 60,611,258 (28.84%)
Unique cis fend pairs 22,737,997
Unique trans fend pairs 50,764,031

Insert Size Distribution

Fend Intra-chromosomal Interaction Distribution

Fend Inter-chromosomal Interaction Distribution

Best insert size

586